BioPortal Help - Revision history

JenniferVendetti: /* BioPortal */

2026-01-13T21:21:59Z

BioPortal

JenniferVendetti: /* How to cite NCBO and BioPortal */ Reorder sub-sections with most relevant at the top

2026-01-13T21:21:06Z

How to cite NCBO and BioPortal: Reorder sub-sections with most relevant at the top

JenniferVendetti: /* BioPortal */ Update cite to new NAR paper

2026-01-13T21:19:46Z

BioPortal: Update cite to new NAR paper

JenniferVendetti: /* NCBO Ontology Recommender */ Remove reference to "NCBO", which is now defunct

2026-01-13T21:14:26Z

NCBO Ontology Recommender: Remove reference to "NCBO", which is now defunct

JenniferVendetti: /* Ontology visibility options */

2025-01-07T21:19:24Z

Ontology visibility options

JenniferVendetti: /* Projects */ Fix button name to reflect current UI

2025-01-07T21:15:59Z

Projects: Fix button name to reflect current UI

JenniferVendetti: /* Homepage */ Fix broken nav links

2025-01-07T21:12:25Z

Homepage: Fix broken nav links

JenniferVendetti: /* Ontologies */ Improve flow of sections and add headings for readability

2025-01-07T21:10:25Z

Ontologies: Improve flow of sections and add headings for readability

JenniferVendetti: /* Browsing */ Remove outdated descriptions of how licensed and private ontologies are accessed

2025-01-07T20:18:47Z

Browsing: Remove outdated descriptions of how licensed and private ontologies are accessed

JenniferVendetti: /* Browsing */

2025-01-07T20:04:41Z

Browsing

@@ Line 219: / Line 219: @@
 === BioPortal ===
-Jennifer Vendetti, Nomi L Harris, Michael V Dorf, Alex Skrenchuk, J Harry Caufield, Rafael S Goncalves, John B Graybeal, Harshad Hegde, Timothy Redmond, Christopher J Mungall, Mark A Musen. BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies. ''Nucleic Acids Research'', Volume 53, Issue W1, 7 July 2025, Pages W84-W94, https://academic.oup.com/nar/article/53/W1/W84/8129374
+Jennifer Vendetti, Nomi L Harris, Michael V Dorf, Alex Skrenchuk, J Harry Caufield, Rafael S Goncalves, John B Graybeal, Harshad Hegde, Timothy Redmond, Christopher J Mungall, Mark A Musen. BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies. ''Nucleic Acids Research'', Volume 53, Issue W1, 7 July 2025, Pages W84-W94, https://academic.oup.com/nar/article/53/W1/W84/8129374.
 === Ontology Recommender ===

@@ Line 217: / Line 217: @@
 == How to cite NCBO and BioPortal ==
-=== NCBO ===
-Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.
+=== BioPortal ===
 === Ontology Recommender ===
 Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).
-=== BioPortal ===
+=== NCBO ===
+Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.
 === SPARQL Endpoint ===
 Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.

@@ Line 224: / Line 224: @@
 === BioPortal ===
-Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.
 === SPARQL Endpoint ===
 Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.

@@ Line 220: / Line 220: @@
 Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.
-===NCBO Ontology Recommender===
+=== Ontology Recommender ===
 Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).

@@ Line 28: / Line 28: @@
 ==== Ontology visibility options ====
-Submitters can control who can browse the terms in their ontology by selecting one of three visibility designations when uploading:
+Submitters control who can browse the terms in their ontology by selecting one of three visibility designations when uploading:
 * '''Public:''' The ontology and its metadata are fully visible and accessible to all users.

@@ Line 91: / Line 91: @@
 === Projects ===
-This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.
+This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create new project" button. Note that you must be logged in to BioPortal to create a project.
 == Common Tasks ==

@@ Line 3: / Line 3: @@
 BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
-* [[#Browse Tab|browse the library]] of ontologies
+* [[#Ontologies|browse the library]] of ontologies
-* [[#Search Tab|search for a term]] across multiple ontologies
+* [[#Search|search for a term]] across multiple ontologies
-* [[#Mappings Tab|browse mappings]] between terms in different ontologies
+* [[#Mappings|browse mappings]] between terms in different ontologies
-* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus
+* [[#Recommender|receive recommendations]] on which ontologies are most relevant for a corpus
-* [[#Annotator Tab|annotate text]] with terms from ontologies
+* [[#Annotator|annotate text]] with terms from ontologies
-* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources
+* [[#Projects|browse a selection of projects]] that use BioPortal resources
-All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.
+All information available through the BioPortal website is also available through the BioPortal REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.
 === Ontologies ===

@@ Line 14: / Line 14: @@
 === Ontologies ===
-==== Browsing ====
+==== Browsing biomedical ontologies ====
-Browse our library of biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.
+Explore our library of biomedical ontologies or submit your own. The ontology browse page provides summary information about each ontology. For more detailed information, visit the ontology’s dedicated page by clicking its name.
-To '''quickly find a specific ontology''', type its name or abbreviation into the search field at the top-center of the page, labeled “Search…”. You can also narrow the results using the faceted browsing elements on the left-hand side of the page. These facets allow you to filter ontologies by criteria such as category (domain), group, format, or other attributes.
+==== Finding an ontology ====
-To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology.
+==== Ontology popularity ====
-Some submitters want to control who can browse the terms in their ontology. When uploading an ontology to BioPortal, submitters can choose from three visibility designations:
+Ontologies on this page are ordered by popularity, determined by the number of Google Analytics page views they received in the previous month. Ontologies with more views appear higher in the list, helping you quickly locate the most widely accessed resources.
 * '''Public:''' The ontology and its metadata are fully visible and accessible to all users.
@@ Line 28: / Line 35: @@
 These designations allow submitters to control the visibility and accessibility of their ontologies based on their sharing preferences and requirements.
 ==== Programmatic access ====
-To '''access ontologies programmatically''', see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Media Types).
+To access ontologies programmatically, see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Available Media Types).
 === Search ===

@@ Line 21: / Line 21: @@
 To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology.
-Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both
+Some submitters want to control who can browse the terms in their ontology. When uploading an ontology to BioPortal, submitters can choose from three visibility designations:
-* logged in to BioPortal
-* granted access to the ontology
+* '''Public:''' The ontology and its metadata are fully visible and accessible to all users.
-For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.
+* '''Private:''' The ontology is restricted and only accessible to user accounts explicitly granted access by the submitter.
 ==== Popularity ====